The Differential Immune Responses to COVID-19 in Peripheral and Lung
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Gene Expression, Network Analysis, and Drug Discovery of Neurofibromatosis Type 2-Associated Vestibular Schwannomas Based on Bioinformatics Analysis
Hindawi Journal of Oncology Volume 2020, Article ID 5976465, 9 pages https://doi.org/10.1155/2020/5976465 Research Article Gene Expression, Network Analysis, and Drug Discovery of Neurofibromatosis Type 2-Associated Vestibular Schwannomas Based on Bioinformatics Analysis Qiao Huang , Si-Jia Zhai , Xing-Wei Liao , Yu-Chao Liu, and Shi-Hua Yin Department of Otolaryngology & Head and Neck Surgery, e Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, China Correspondence should be addressed to Shi-Hua Yin; [email protected] Received 26 March 2020; Revised 27 May 2020; Accepted 1 June 2020; Published 15 July 2020 Academic Editor: Pierfrancesco Franco Copyright © 2020 Qiao Huang et al. ,is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Neurofibromatosis Type 2- (NF2-) associated vestibular schwannomas (VSs) are histologically benign tumors. ,is study aimed to determine disease-related genes, pathways, and potential therapeutic drugs associated with NF2-VSs using the bioinformatics method. Microarray data of GSE108524 were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were screened using GEO2R. ,e functional enrichment and pathway enrichment of DEGs were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG). Furthermore, the STRING and Cytoscape were used to analyze the protein-protein interaction (PPI) network of all differentially expressed genes and identify hub genes. Finally, the enriched gene sets belonging to the identified pathways were queried against the Drug-Gene Interaction database to find drug candidates for topical use in NF2-associated VSs. -
Variation in FCN1 Affects Biosynthesis of Ficolin-1 and Is Associated With
Genes and Immunity (2012) 13, 515–522 & 2012 Macmillan Publishers Limited All rights reserved 1466-4879/12 www.nature.com/gene ORIGINAL ARTICLE Variation in FCN1 affects biosynthesis of ficolin-1 and is associated with outcome of systemic inflammation L Munthe-Fog1, T Hummelshoj1, C Honore´ 1, ME Moller1, MO Skjoedt1, I Palsgaard1, N Borregaard2, HO Madsen1 and P Garred1 Ficolin-1 is a recognition molecule of the lectin complement pathway. The ficolin-1 gene FCN1 is polymorphic, but the functional and clinical consequences are unknown.The concentration of ficolin-1 in plasma and FCN1 polymorphisms in positions À 1981 (rs2989727), À 791 (rs28909068), À 542 (rs10120023), À 271 (rs28909976), À 144 (rs10117466) and þ 7918 (rs1071583) were determined in 100 healthy individuals. FCN1 expression by isolated monocytes and granulocytes and ficolin-1 levels in monocyte culture supernatants were assessed in 21 FCN1-genotyped individuals. FCN1 polymorphisms were determined in a cohort of 251 patients with systemic inflammation. High ficolin-1 plasma levels were significantly associated with the minor alleles in position À 542 and À 144. These alleles were also significantly associated with high FCN1 mRNA expression. The level of ficolin-1 in culture supernatants was significantly higher in individuals homozygous for the minor alleles at positions À 542 and À 144. Homozygosity for these alleles was significantly associated with fatal outcome in patients with systemic inflammation. None of the other investigated polymorphisms were associated with FCN1 and ficolin-1 expression, concentration or disease outcome. Functional polymorphic sites in the promoter region of FCN1 regulate both the expression and synthesis of ficolin-1 and are associated with outcome in severe inflammation. -
Associations Between FCGR3A Polymorphisms and Susceptibility to Rheumatoid Arthritis: a Metaanalysis YOUNG HO LEE, JONG DAE JI, and GWAN GYU SONG
Associations Between FCGR3A Polymorphisms and Susceptibility to Rheumatoid Arthritis: A Metaanalysis YOUNG HO LEE, JONG DAE JI, and GWAN GYU SONG ABSTRACT. Objective. To investigate whether the Fcγ receptor (FCGR) polymorphism confers susceptibility to rheumatoid arthritis (RA). Methods. We conducted metaanalyses on the associations between FCGR polymorphisms and RA susceptibility as determined using (1) allele contrast, (2) recessive models, (3) dominant models, and (4) contrast of homozygotes, using fixed or random effects models. Results. A total of 10 separate comparisons were considered, which comprised 6 European and 4 Asian population samples. Metaanalysis of FCGR3A polymorphism revealed a significant associa- tion between the VV genotype and the risk of developing RA relative to the VF+FF genotype (OR 1.256, 95% CI 1.045–1.510, p = 0.015), with no evidence of between-study heterogeneity (p = 0.167). In subjects of European descent, a stronger association was observed between the VV geno- type and RA than for the FF genotype (OR 1.374, 95% CI 1.101–1.714, p = 0.005). In Asians, no such association was found. Metaanalysis of the VV vs FF genotype revealed a significantly increased OR in Europeans (OR 1.399, 95% CI 1.107–1.769, p = 0.005), but not in Asians. No asso- ciation was found between RA and the FCGR2A and FCGR3B polymorphisms in all subjects and in European and Asian populations, except for the NA22 vs NA11 of FCGR3B in Europeans. Conclusion. No relation was found between the FCGR2A polymorphism and susceptibility to RA in Europeans or Asians. The FCGR3A polymorphism was found to be associated with RA in Europeans but not in Asians. -
Human Lectins, Their Carbohydrate Affinities and Where to Find Them
biomolecules Review Human Lectins, Their Carbohydrate Affinities and Where to Review HumanFind Them Lectins, Their Carbohydrate Affinities and Where to FindCláudia ThemD. Raposo 1,*, André B. Canelas 2 and M. Teresa Barros 1 1, 2 1 Cláudia D. Raposo * , Andr1 é LAQVB. Canelas‐Requimte,and Department M. Teresa of Chemistry, Barros NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829‐516 Caparica, Portugal; [email protected] 12 GlanbiaLAQV-Requimte,‐AgriChemWhey, Department Lisheen of Chemistry, Mine, Killoran, NOVA Moyne, School E41 of ScienceR622 Co. and Tipperary, Technology, Ireland; canelas‐ [email protected] NOVA de Lisboa, 2829-516 Caparica, Portugal; [email protected] 2* Correspondence:Glanbia-AgriChemWhey, [email protected]; Lisheen Mine, Tel.: Killoran, +351‐212948550 Moyne, E41 R622 Tipperary, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +351-212948550 Abstract: Lectins are a class of proteins responsible for several biological roles such as cell‐cell in‐ Abstract:teractions,Lectins signaling are pathways, a class of and proteins several responsible innate immune for several responses biological against roles pathogens. such as Since cell-cell lec‐ interactions,tins are able signalingto bind to pathways, carbohydrates, and several they can innate be a immuneviable target responses for targeted against drug pathogens. delivery Since sys‐ lectinstems. In are fact, able several to bind lectins to carbohydrates, were approved they by canFood be and a viable Drug targetAdministration for targeted for drugthat purpose. delivery systems.Information In fact, about several specific lectins carbohydrate were approved recognition by Food by andlectin Drug receptors Administration was gathered for that herein, purpose. plus Informationthe specific organs about specific where those carbohydrate lectins can recognition be found by within lectin the receptors human was body. -
Adiponectin and Related C1q/TNF-Related Proteins Bind Selectively to Anionic Phospholipids and Sphingolipids
Adiponectin and related C1q/TNF-related proteins bind selectively to anionic phospholipids and sphingolipids Jessica J. Yea,b, Xin Bianc,d, Jaechul Lima,b, and Ruslan Medzhitova,b,1 aHHMI, Yale University, New Haven, CT 06520; bDepartment of Immunobiology, Yale University School of Medicine, New Haven, CT 06520; cDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT 06520; and dDepartment of Neuroscience, Yale University School of Medicine, New Haven, CT 06520 Contributed by Ruslan Medzhitov, April 14, 2020 (sent for review December 20, 2019; reviewed by Ido Amit and G. William Wong) Adiponectin (Acrp30) is an adipokine associated with protection 5-mers of trimers, respectively referred to as low molecular weight from cardiovascular disease, insulin resistance, and inflammation. (LMW), medium molecular weight (MMW), and high molecular Although its effects are conventionally attributed to binding weight (HMW) complexes. Adiponectin can also be cleaved by Adipor1/2 and T-cadherin, its abundance in circulation, role in serum elastases and thrombin between the globular C1q-like head ceramide metabolism, and homology to C1q suggest an overlooked domain and the collagenous tail domain, forming globular adi- role as a lipid-binding protein, possibly generalizable to other C1q/ ponectin (gAd). While gAd appears to bind AdipoR1/2 and ac- TNF-related proteins (CTRPs) and C1q family members. To investi- tivate AMPK more strongly than full-length protein (19, 20), levels gate this, adiponectin, representative family members, and variants of HMW multimers are more strongly associated with insulin were expressed in Expi293 cells and tested for binding to lipids in sensitivity (21, 22), have a longer half-life in circulation (18), and liposomes using density centrifugation. -
Microarray Analysis of Novel Genes Involved in HSV- 2 Infection
Microarray analysis of novel genes involved in HSV- 2 infection Hao Zhang Nanjing University of Chinese Medicine Tao Liu ( [email protected] ) Nanjing University of Chinese Medicine https://orcid.org/0000-0002-7654-2995 Research Article Keywords: HSV-2 infection,Microarray analysis,Histospecic gene expression Posted Date: May 12th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-517057/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background: Herpes simplex virus type 2 infects the body and becomes an incurable and recurring disease. The pathogenesis of HSV-2 infection is not completely clear. Methods: We analyze the GSE18527 dataset in the GEO database in this paper to obtain distinctively displayed genes(DDGs)in the total sequential RNA of the biopsies of normal and lesioned skin groups, healed skin and lesioned skin groups of genital herpes patients, respectively.The related data of 3 cases of normal skin group, 4 cases of lesioned group and 6 cases of healed group were analyzed.The histospecic gene analysis , functional enrichment and protein interaction network analysis of the differential genes were also performed, and the critical components were selected. Results: 40 up-regulated genes and 43 down-regulated genes were isolated by differential performance assay. Histospecic gene analysis of DDGs suggested that the most abundant system for gene expression was the skin, immune system and the nervous system.Through the construction of core gene combinations, protein interaction network analysis and selection of histospecic distribution genes, 17 associated genes were selected CXCL10,MX1,ISG15,IFIT1,IFIT3,IFIT2,OASL,ISG20,RSAD2,GBP1,IFI44L,DDX58,USP18,CXCL11,GBP5,GBP4 and CXCL9.The above genes are mainly located in the skin, immune system, nervous system and reproductive system. -
Single‑Nucleotide Polymorphisms and Copy Number Variations of the FCGR2A and FCGR3A Genes in Healthy Japanese Subjects
BIOMEDICAL REPORTS 2: 265-269, 2014 Single‑nucleotide polymorphisms and copy number variations of the FCGR2A and FCGR3A genes in healthy Japanese subjects HIROYUKI MORIYA1, KATSUHIKO SAITO1,2, NUALA HELSBY3, NAOMI HAYASHI1, SHIGEKAZU SUGINO4, MICHIAKI YAMAKAGE4, TAKERU SAWAGUCHI5, MASAHIKO TAKASAKI5, MASATO TAKAHASHI6 and NAHOKO KUROSAWA1 1Department of Pharmacy, Hokkaido Pharmaceutical University School of Pharmacy, Otaru, Hokkaido 047-0264; 2Department of Pharmacy, Sapporo Hokuyu Hospital, Sapporo, Hokkaido 003-0006, Japan; 3Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1142, New Zealand; 4Department of Anesthesiology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543; Departments of 5Pharmacy and 6Breast Surgery, National Hospital Organization Hokkaido Cancer Center, Sapporo, Hokkaido 003-0804, Japan Received October 24, 2013; Accepted November 18, 2013 DOI: 10.3892/br.2013.210 Abstract. FcγRII and FcγRIII are low-affinity Fcγ recep- previous findings regarding FCGR2A and FCGR3A alleles and tors that are encoded by the FCGR2A and FCGR3A genes, CNVs. These assays may provide a basis for the investigation of respectively. These genes contain functional single-nucleotide the role of these genes in the efficacy of antibody-based drugs, polymorphisms (SNPs), which alter the binding affinities of such as trastuzumab and rituximab, in Japanese subjects. these receptors for the γ chain of the Fc fragment of immu- noglobulin G. The known SNPs in FCGR2A and FCGR3A Introduction are rs1801274 (A>G; H131R) and rs396991 (T>G; F158V), respectively. It is also known that there are copy number varia- Fcγ receptors (FcγRs) bind specifically to the γ chain of the tions (CNVs) in the genetic locus (1q23) where FCGR2A and Fc fragment of immunoglobulin G (IgG) and are located on the FCGR3A are located. -
Integrated Weighted Gene Co-Expression Network Analysis Identi Ed That TLR2 and CD40 Are Related to Coronary Artery Disease
Integrated weighted gene co-expression network analysis identied that TLR2 and CD40 are related to coronary artery disease Bin Qi Liuzhou People's Hospital Jian-Hong Chen Liuzhou People's Hospital Lin Tao Liuzhou People's Hospital Chuan-Meng Zhu Liuzhou People's Hospital Yong Wang Liuzhou People's Hospital Guo-Xiong Deng The First People's of Nanning Liu Miao ( [email protected] ) LiuZhou People's Hospital https://orcid.org/0000-0001-6642-7005 Research article Keywords: Gene Expression Omnibus, Integrated weighted gene co-expression network analysis (WGCNA), Functional enrichment, Functional validation and prognostic analysis. Posted Date: October 7th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-86115/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/16 Abstract Background: The current research attempted to identify possible hub genes and pathways of coronary artery disease (CAD) and to detect the possible mechanisms. Methods: Array data from GSE90074 were downloaded from the Gene Expression Omnibus (GEO) database. Integrated weighted gene co-expression network analysis (WGCNA) was performed to analyze the gene module and clinical characteristics. Gene Ontology annotation, Disease Ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed by clusterProler and the DOSE package in R. A protein-protein interaction (PPI) network was established using Cytoscape software, and signicant modules were analyzed using Molecular Complex Detection to identify hub genes. Then, further functional validation of hub genes in other microarrays and population samples was performed, and survival analysis was performed to investigate the prognosis. -
First Infusion Reactions Are Mediated by Fcγriiib and Neutrophils
Pharm Res (2018) 35: 169 https://doi.org/10.1007/s11095-018-2448-8 RESEARCH PAPER First Infusion Reactions are Mediated by FcγRIIIb and Neutrophils Felix Weber 1 & Daniel Breustedt 1,2 & Sonja Schlicht 3 & Claas A. Meyer 3 & Jens Niewoehner 4 & Martin Ebeling 1 & Per-Ola Freskgard5 & Peter Bruenker6 & Thomas Singer1 & Michael Reth7 & Antonio Iglesias1 Received: 29 March 2018 /Accepted: 15 June 2018 /Published online: 27 June 2018 # The Author(s) 2018 ABSTRACT FIR. FcγRIIIb-mediated FIR was abolished by depleting neu- Purpose Administration of therapeutic monoclonal antibod- trophils or blocking FcγRIIIb with CD11b antibodies. ies (mAbs) is frequently accompanied by severe first infusion Conclusions Human FcγRIIIb and neutrophils are primarily reactions (FIR). The mechanism driving FIR is still unclear. responsible for triggering FIR. Clinical strategies to prevent This study aimed to investigate the cellular and molecular FIR in patients should focus on this pathway and may include mechanisms causing FIR in humanized mouse models and transient depletion of neutrophils or blocking FcγRIIIb with their potential for evaluating FIR risk in patients. specific mAbs. Methods Mice humanized for Fc gamma receptors (FcγRs) were generated by recombination-mediated genomic replace- KEY WORDS human FcγRIIIb . humanized mouse model . ment. Body temperature, cytokine release and reactive oxygen immunotoxicology . infusion reactions . neutrophils species (ROS) were measured to assess FIR to mAbs. Results Infusion of human mAb specific for mouse transferrin receptor (HamTfR) into FcγR-humanized mice, produced marked transient hypothermia accompanied by an increase ABBREVIATIONS in inflammatory cytokines KC and MIP-2, and ROS. FIR ADA Anti-drug antibodies were dependent on administration route and Fc-triggered ef- ADCC Antibody-dependent cellular cytotoxicity fector functions mediated by neutrophils. -
Type of the Paper (Article
Supplementary figures and tables E g r 1 F g f2 F g f7 1 0 * 5 1 0 * * e e e * g g g * n n n * a a a 8 4 * 8 h h h * c c c d d d * l l l o o o * f f f * n n n o o o 6 3 6 i i i s s s s s s e e e r r r p p p x x x e e e 4 2 4 e e e n n n e e e g g g e e e v v v i i i t t t 2 1 2 a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d J a k 2 N o tc h 2 H if1 * 3 4 6 * * * e e e g g g n n n a a * * a * h h * h c c c 3 * d d * d l l l * o o o f f 2 f 4 n n n o o o i i i s s s s s s e e e r r 2 r p p p x x x e e e e e e n n n e e 1 e 2 g g g e e 1 e v v v i i i t t t a a a l l l e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Z e b 2 C d h 1 S n a i1 * * 7 1 .5 4 * * e e e g g g 6 n n n * a a a * h h h c c c 3 * d d d l l l 5 o o o f f f 1 .0 * n n n * o o o i i i 4 * s s s s s s e e e r r r 2 p p p x x x 3 e e e e e e n n n e e e 0 .5 g g g 2 e e e 1 v v v i i i t t t a a a * l l l e e e 1 * R R R 0 0 .0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d M m p 9 L o x V im 2 0 0 2 0 8 * * * e e e * g g g 1 5 0 * n n n * a a a * h h h * c c c 1 5 * 6 d d d l l l 1 0 0 o o o f f f n n n o o o i i i 5 0 s s s s s s * e e e r r r 1 0 4 3 0 p p p * x x x e e e * e e e n n n e e e 2 0 g g g e e e 5 2 v v v i i i t t t a a a l l l 1 0 e e e R R R 0 0 0 c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d c o n tro l u n in fla m e d in fla m e d Supplementary Figure 1. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Arming Tumor-Associated Macrophages to Reverse Epithelial
Published OnlineFirst August 15, 2019; DOI: 10.1158/0008-5472.CAN-19-1246 Cancer Tumor Biology and Immunology Research Arming Tumor-Associated Macrophages to Reverse Epithelial Cancer Progression Hiromi I.Wettersten1,2,3, Sara M.Weis1,2,3, Paulina Pathria1,2,Tami Von Schalscha1,2,3, Toshiyuki Minami1,2,3, Judith A. Varner1,2, and David A. Cheresh1,2,3 Abstract Tumor-associated macrophages (TAM) are highly expressed it engaged macrophages but not natural killer (NK) cells to within the tumor microenvironment of a wide range of cancers, induce antibody-dependent cellular cytotoxicity (ADCC) of where they exert a protumor phenotype by promoting tumor avb3-expressing tumor cells despite their expression of the cell growth and suppressing antitumor immune function. CD47 "don't eat me" signal. In contrast to strategies designed Here, we show that TAM accumulation in human and mouse to eliminate TAMs, these findings suggest that anti-avb3 tumors correlates with tumor cell expression of integrin avb3, represents a promising immunotherapeutic approach to redi- a known driver of epithelial cancer progression and drug rect TAMs to serve as tumor killers for late-stage or drug- resistance. A monoclonal antibody targeting avb3 (LM609) resistant cancers. exploited the coenrichment of avb3 and TAMs to not only eradicate highly aggressive drug-resistant human lung and Significance: Therapeutic antibodies are commonly engi- pancreas cancers in mice, but also to prevent the emergence neered to optimize engagement of NK cells as effectors. In of circulating tumor cells. Importantly, this antitumor activity contrast, LM609 targets avb3 to suppress tumor progression in mice was eliminated following macrophage depletion.